8PUL | pdb_00008pul

ChiLob 7/4 H2 HC-K223C/C224S Kappa LC-C214S F(ab')2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6TKE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	294.15	0.1M TRIS, 15% PEG 4000, 15% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.995	α = 90
b = 95.818	β = 90
c = 151.924	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	45	PIXEL	DECTRIS PILATUS 12M		2022-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I23	2.7552	Diamond	I23

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.93	151.92	85.72	0.058	0.061	0.018	0.997	16.93	9.58		71110

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.93	1.97	73.7		1.879	2.025	0.729	0.274	0.283	7.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.93	81.177	71045	3525	85.644	0.205	0.2029	0.2049	0.2387	0.242	61.604

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-1.042			2.551		-1.509

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.209
r_dihedral_angle_3_deg	10.896
r_lrange_it	7.83
r_lrange_other	7.83
r_dihedral_angle_1_deg	7.333
r_scangle_it	5.44
r_scangle_other	5.439
r_dihedral_angle_2_deg	4.997
r_mcangle_other	4.491
r_mcangle_it	4.489
r_scbond_it	3.569
r_scbond_other	3.569
r_mcbond_it	2.928
r_mcbond_other	2.926
r_angle_refined_deg	0.794
r_angle_other_deg	0.298
r_symmetry_nbd_refined	0.234
r_nbd_other	0.216
r_symmetry_nbd_other	0.189
r_nbd_refined	0.171
r_nbtor_refined	0.169
r_symmetry_xyhbond_nbd_refined	0.161
r_xyhbond_nbd_refined	0.126
r_ncsr_local_group_1	0.095
r_ncsr_local_group_2	0.083
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.039
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6632
Nucleic Acid Atoms
Solvent Atoms	322
Heterogen Atoms	18

Software

Software
Software Name	Purpose
REFMAC	refinement
GDA	data collection
DIALS	data reduction
xia2	data scaling
MOLREP	phasing
Coot	model building